Gene expression in the brain is important for understanding the genetic control of brain development. Because the laboratory mouse shares many genes and disease loci with human, its gene expression patterns are important for research in this area. With modern high throughput techniques, large scale gene expression data in the mouse brain are becoming available, and several mouse gene expression databases are being established. To integrate and analyze gene expression data with neuroanatomy in the embryonic and neonatal mouse brains, it is necessary to create three dimensional reference atlases of the developing mouse brain and tools that can map gene expression data into the atlas and perform analysis and visualization. The proposed study will establish a series of three dimensional reference atlases of the developing mouse brain based on high spatial resolution and rich tissue contrast provided by modern magnetic resonance imaging techniques. The atlases will contains structural annotation/segmentation, and more importantly, information on morphological changes during development obtained using advanced computational techniques. The proposed study will also develop tools that mapping gene expression data to the reference atlases. A selected group of gene expressions will be mapped, validated, and studied. The mapped gene expression data will also help us to define more detailed structures in the developing mouse brain atlases.